LOS CONSORCIOS DE INOVACION: Programa GENOMA, Rede ONSA

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LOS CONSORCIOS DE INOVACION Programa GENOMA,
Rede ONSA
Programa Cooperativo para el Desarrollo
Tecnológico Agroalimentario y Agroindustrial del
Cono Sur
Argentina Chile Bolivia Paraguay Brasil Uruguay

• Paulo Arruda
• Centro de Biología Molecular e Engenharia
  Genética
• Universidade Estadual de Campinas
• Brasil

Banco Interamericano de Desarrollo
SEMINARIO-TALLER INTERNACIONAL
Departamento de Desarrollo Sostenible Unidad de
Desarrollo Rural
Gestión de la integración tecnológica y
cooperación regional en el sistema
agroalimentario y agroindustrial del MERCOSUR
ampliado Setiembre 13-14, 2001 - Montevideo,
Uruguay
Departamento de Integración y Programas Regionales
Instituto para la Integración de América Latina
y el Caribe
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THE ONSA NETWORK

• 65 Sequencing labs
• 5 Bioinformatic labs
• 80 Data mining groups or bioinformatic
  associates
• 1 Clone storage and distribution lab
• BCCC - Brazilian Clone Collection Center
• 5 Expression profile labs equipped with
• spotters and scanners
• Total people involved 400

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FAPESP Genome Program

• Organism Size Funding Start
  Status
• Xyllela fastidiosa CVC (Orange) 2.7 Mb
  Fapesp 04/1998 Published
  Fundicitrus
• Xanthomonas citri (Orange) 5.4 Mb
  Fapesp 03/1999 Closed
  
  Fundicitrus
• Xanthomonas campestris 5.4 Mb Fapesp
  03/1999 Closed
  
  Fundicitrus
• Xyllela fastidiosa PD (Grape) 2.7 Mb
  Fapesp 09/2000 Closed
  
  USDA
• Leifisonia xyli (Sugarcane) 2.9 Mb
  Fapesp 09/2000 In progress
  ICSB
• Sugarcane ESTs Fapesp
  07/1999 Finished
  
  Copersucar
• Human cancer ESTs Fapesp
  03/1999 In progress Ludwig Inst.

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CANA DE AÇÚCAR NO BRASIL

• 25 da produção mundial
• 300 milhões de toneladas
• 5 milhões de hectares
• 14.5 milhões de tonedas de açucar
• 15.3 bilhões de litros de alcool
• 350 indústrias
• 50 mil produtores
• 1.4 milhões de empregod diretos
• 3.6 milhões de empregos indiretos

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SUCEST

• - Coordenador Geral
• - Cooperação Internacional
• - Bioinformatica
• - Laboratórios de Sequenciamento (22)
• - Grupos de Data Mining (48)
• - Laboratório de Armazenagem e Distribuição

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BIBLIOTECAS de cDNA

• Tecidos No bibliotecas
• Casca 1
• Cartucho 2
• Zona de transição raiz parte aérea 3
• Gemas laterais 2
• Folhas jovens 1
• Raiz 3
• Colmo 3
• Callus 7
• Sementes em desenvolvimento 2
• Meristema apical 2
• Plantas infectadas com Herbaspirilum
  rubrisubalbicans 1
• Plantas infectadas com Acetobacter
  diazotrophicus 1
• Flores em desenvolvimento 7
• Pool de bibliotecas normalizadas
  2
• Total 37

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LABORATORIOS DE SEQUENCIAMENTO
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EST Clustering and Contiging
ESTs analyzed 291,669 ESTs after
triming and quality control 237,954
Clusters (C) 26,303
Singletons (S) 16,838 CS
with significant matches in GenBank
23,296 CS without significant matches in
GenBank 19,845 CS with full length
insert 14,409 Clusters with tentative
full consensus sequence 9,045
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EST Clustering and Contiging
ESTs analyzed 291,669 ESTs after
triming and quality control 237,954
Clusters (C) 26,303
Singletons (S) 16,838 CS with
significant matches in GenBank 23,296
CS without significant matches in GenBank
19,845 CS with full length insert
14,409 Clusters with tentative full
consensus sequence 9,045
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DATA MINING
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GRUPOS DE DATA MINING

• IAC Campinas, SP. Finding genes related to
  nematode resistance in sugarcane
• UFAL Alagoas, Al. Identification of genes
  related to water stress resistance
• UNESP Araraquara, SP. dentification of heat
  shock proteins
• UESC Ilheus, BA. Identification of genes
  involved in the secretory pathway
• UNESP Botucatu, SP. ESTs Involved in the
  Response Mechanisms Induced by Pathogens
• UNESP Botucatu, SP. Metabolic pathway of
  sugars involved in boron mobility
• CBMEG Campinas, SP. Prospection of sugarcane
  transcription factors
• CENA Piracicaba, SP. Sugarcane genes involved
  in nutrient uptake and metal resistance
• CBMEG Campinas, SP. Data Mining of Sugarcane
  Glycosylation Enzymes
• COPERSUCAR Piracicaba, SP. Sugarcane genes
  involved in sucrose metabolism
• COPERSUCAR Piracicaba, SP. Microssatellite
  Data Mining
• CBMEG Campinas, SP. Sugarcane genes involved
  in aluminum tolerance
• ESALQ Piracicaba, SP. Characterization of
  genes involved in flower development
• ESALQ Piracicaba, SP. Insect resistant genes
• EMBRAPA Sete Lagoas, MG. Aluminum Tolerance
  in Grasses Using Sugarcane ESTs
• ESALQ Piracicaba, SP. Finding the homologs of
  sugarcane stress-related genes

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GRUPOS DE DATA MINING

• ESALQ Piracicaba, SP. The sugarcane
  transcription factors
• ESALQ Piracicaba, SP. Identification of
  proteins involved in of plant-microbe
  interactions
• ESALQ Piracicaba, SP. Genes involved in
  photosynthesis.
• USP São Paulo, SP. Finding genes related with
  cell wall proteins in sugar cane
• USP São Paulo, SP. DNA repair genes in
  sugarcane
• UNESP Jaboticabal, SP. Sugarcane genes
  related to water stress
• UNESP Jaboticabal, SP. Sugarcane genes
  involved in carbohydrates metabolism
• UNESP Jaboticabal, SP. Sugarcane Genes
  Involved in Vacuolar Sucrose Storage
• LABJOR Campinas, SP. Midia/Ciência of Sugar
  Cane Genome Project
• LNLS Campinas, SP. Chaperones, HSPs and other
  stress related proteins
• UMC Mogi das Cruzes, SP. Genes involved in
  Programmed Cell Death
• UFRNET Natal, RN. Search for the sugarcane
  base excision repair genes
• UENF Campos, RJ. Stress-related genes in
  sugarcane
• UFPE Recife, PE. HSP70 and cognate proteins
  differential expression in sugar cane
• UFPE Recife, PE. Identification of RGAs
  (Resistance Gene Analogs) in sugarcane
• IPA Recife, PE. Sugarcane genes related with
  plant defense mechanisms
• UFPE Recife, PE. Sugarcane genes involved in
  male fertility

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GRUPOS DE DATA MINING

• TECPAR Londrina, PN. Plant secondary
  metabolites
• USP São Paulo, SP. Signal transduction
  components of the sugarcane genome
• USP São Paulo, SP. Membrane Receptors -
  Elements of signalization
• USP Ribeirão Preto, SP. Genes involved in
  sugarcane flower development
• UFRJ Rio de Janeiro, RJ. Glycine-Rich
  Proteins and Enzymes of Lignin Metabolism
• UFRJ Rio de Janeiro, RJ. Cell cycle and
  nitrogen metabolism in sugarcane
• UNESP Rio Claro, SP. Markers for sugarcane
  evolution
• UFRJ Rio de Janeiro, RJ. Sugarcane Cysteine
  Proteinase and Phytocystatins
• UNAERP Ribeirão Preto, SP. Biosynthesis of
  secondary metabolites and biopolymers
• UNAERP Ribeirão Preto, SP. Bacterial-like
  two-component regulator genes
• UFSCAR São Carlos, SP. Metalloprotease Gene
  Families in Sugar Cane
• UFSCAR São Carlos, SP. Genes Associated With
  Plant Defense mechanisms
• USP São Carlos, SP. Purine synthesis pathway
  and identification of novel genes
• USP São Paulo, SP. Oxidative stress response
  in sugar cane
• USP São Paulo, SP. Retrotransposons and
  NBS-LRR gene families in sugarcane
• UNIVAP São José dos Campos, SP. Agents for
  Navigation Aid in Genome Databases
• UNIVAP São José dos Campos, SP. Sugarcane
  genes related to mitochondrial function

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COMPARATIVE GENOMICS
Clusters Singletons analyzed
33,507 Significant matches with Arabidopsis
thaliana ESTs 15,240 (45) No
matches with Arabidopsis thaliana ESTs
18,267 (55) Significant matches with
Arabidopsis thaliana Genome
3,600 (11) Significant matches with
predict At genes 3,324
Significant matches with unpredicted At genes
276 No matches with
Arabidopsis thaliana 14,667
(44) No matches with plant genes
9,305 Significant
matches with other plants
5,362 Exclusive matches with monocots
4,891 (15)
Exclusive matches with other dicots
67 Matches with dicots
and monocots 404
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MECANISMOS DE RESPOSTA AO FRIO

• Ajustamento do metabolismo
• Indução de tolerância

Alteração da expressão gênica
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GENES INDUZIDOS PELO FRIO




Total de geness induzidos
36


a


14
Genes induzidos por frio


b
8
Genes não relatados induzidos por frio
c

14
Novos genes induzidos por frio
a
Genes previamente relatados como sendo induzidos
por frio


b
Genes que não foram relatados previamente como
sendo induzidos por frio.

c
Genes desconhecidos que não possuem função
descrita.